Roadmap for Microbiota optimisation

What are we trying to achieve and why? What is the problem we are trying to solve?

Investigating the impact of antibiotics/vaccines on the microbiota.
How microbiota affect vaccination.

What are the scientific and technological challenges (knowledge gaps needing to be addressed)?

Understand if antibiotic treatment alters the core microbiota, opening a “door” for pathogen infection (as observed for Salmonella infection in mice and C. diff in humans).
Dose-dependent effects.
Drug-dependent effect.
Age-dependent effect.
Administration route- dependent effect
Identify commonalities among different antibiotics in their effect on metabolic pathways of different bacteria. – as ones with a broad range can have a similar impact on growth as narrow spectrum ones.
Epigenetic of the host (consequence of early antibiotic treatment in the long term in the host) and possible effects on the next generations

What approaches could/should be taken to address the research question?

Study microbiome before and after AB use in different age groups of animals.
Determine which organisms are affected by which antibiotics
Randomised controlled trials comparing impact of different antibiotics.

What else needs to be done before we can solve this need?

Existing knowledge including successes and failures

Administration route- dependent effect: evidence from pigs suggests no difference between oral and systemic administration.
AB use has an impact on the microbiome and therefore on the short chain fatty acids which has a knock-on effect on the microbiome as well as growth performance of the host.